This repository hosts the scripts that were used to assemble the figures of the SNT publication.
These scripts are intended to run from a Fiji installation subscribed to the Neuroanatomy update site, as detailed in the SNT documentation. Scripts relying on sciview/Cx3D functionality, also require the optional subscription to the SciView-Unstable update site. Since data is frequently downloaded from external servers, an internet connection is required.
To simplify execution, we provide ZIP files that pre-bundle an existing Fiji installation with all the required update-site subscriptions. The same ZIP file also contains the contents of this repository. These self-contained ZIP files are provided here.
If instead you prefer to run these scripts on your local Fiji installation, please download the contents of this repository independently using this direct link.
Each figure is associated with a sub-directory of SNTmanuscript (e.g., SNTmanuscript/Fig01/) . The sub-directory then contains one or more scripts. The majority should be run from Fiji, and can be dragged-and-dropped into Fiji's main window: Once displayed in Fiji's script editor, they can be executed by pressing 'Run' (CTRL+R). When relevant, further details are provided on the sub-directory's README.md file.
Note however that some scripts (e.g., in Metrics and FigS6), should be run from a Python environment. Also, please note that not all scripts are self-contained. Some will require separate download of data (e.g., Fig. S1). In those cases, further details are provided on the figure's README.md file. Please do open an issue if you run into problems.